Spaces:
No application file
No application file
File size: 17,141 Bytes
b7731cd |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 |
# Copyright 2006-2016 by Peter Cock. All rights reserved.
# Revisions copyright 2011 Brandon Invergo. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""AlignIO support for "phylip" format from Joe Felsenstein's PHYLIP tools.
You are expected to use this module via the Bio.AlignIO functions (or the
Bio.SeqIO functions if you want to work directly with the gapped sequences).
Support for "relaxed phylip" format is also provided. Relaxed phylip differs
from standard phylip format in the following ways:
- No whitespace is allowed in the sequence ID.
- No truncation is performed. Instead, sequence IDs are padded to the longest
ID length, rather than 10 characters. A space separates the sequence
identifier from the sequence.
Relaxed phylip is supported by RAxML and PHYML.
Note
====
In TREE_PUZZLE (Schmidt et al. 2003) and PHYML (Guindon and Gascuel 2003)
a dot/period (".") in a sequence is interpreted as meaning the same
character as in the first sequence. The PHYLIP documentation from 3.3 to 3.69
http://evolution.genetics.washington.edu/phylip/doc/sequence.html says:
"a period was also previously allowed but it is no longer allowed,
because it sometimes is used in different senses in other programs"
Biopython 1.58 or later treats dots/periods in the sequence as invalid, both
for reading and writing. Older versions did nothing special with a dot/period.
"""
import string
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from .Interfaces import AlignmentIterator
from .Interfaces import SequentialAlignmentWriter
_PHYLIP_ID_WIDTH = 10
_NO_DOTS = "PHYLIP format no longer allows dots in sequence"
class PhylipWriter(SequentialAlignmentWriter):
"""Phylip alignment writer."""
def write_alignment(self, alignment, id_width=_PHYLIP_ID_WIDTH):
"""Use this to write (another) single alignment to an open file.
This code will write interlaced alignments (when the sequences are
longer than 50 characters).
Note that record identifiers are strictly truncated to id_width,
defaulting to the value required to comply with the PHYLIP standard.
For more information on the file format, please see:
http://evolution.genetics.washington.edu/phylip/doc/sequence.html
http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles
"""
handle = self.handle
if len(alignment) == 0:
raise ValueError("Must have at least one sequence")
length_of_seqs = alignment.get_alignment_length()
for record in alignment:
if length_of_seqs != len(record.seq):
raise ValueError("Sequences must all be the same length")
if length_of_seqs <= 0:
raise ValueError("Non-empty sequences are required")
# Check for repeated identifiers...
# Apply this test *after* cleaning the identifiers
names = []
seqs = []
for record in alignment:
"""
Quoting the PHYLIP version 3.6 documentation:
The name should be ten characters in length, filled out to
the full ten characters by blanks if shorter. Any printable
ASCII/ISO character is allowed in the name, except for
parentheses ("(" and ")"), square brackets ("[" and "]"),
colon (":"), semicolon (";") and comma (","). If you forget
to extend the names to ten characters in length by blanks,
the program [i.e. PHYLIP] will get out of synchronization
with the contents of the data file, and an error message will
result.
Note that Tab characters count as only one character in the
species names. Their inclusion can cause trouble.
"""
name = sanitize_name(record.id, id_width)
if name in names:
raise ValueError(
"Repeated name %r (originally %r), possibly due to truncation"
% (name, record.id)
)
names.append(name)
sequence = str(record.seq)
if "." in sequence:
# Do this check here (once per record, not once per block)
raise ValueError(_NO_DOTS)
seqs.append(sequence)
# From experimentation, the use of tabs is not understood by the
# EMBOSS suite. The nature of the expected white space is not
# defined in the PHYLIP documentation, simply "These are in free
# format, separated by blanks". We'll use spaces to keep EMBOSS
# happy.
handle.write(" %i %s\n" % (len(alignment), length_of_seqs))
block = 0
while True:
for name, sequence in zip(names, seqs):
if block == 0:
# Write name (truncated/padded to id_width characters)
# Now truncate and right pad to expected length.
handle.write(name[:id_width].ljust(id_width))
else:
# write indent
handle.write(" " * id_width)
# Write five chunks of ten letters per line...
for chunk in range(0, 5):
i = block * 50 + chunk * 10
seq_segment = sequence[i : i + 10]
# TODO - Force any gaps to be '-' character?
# TODO - How to cope with '?' or '.' in the sequence?
handle.write(f" {seq_segment}")
if i + 10 > length_of_seqs:
break
handle.write("\n")
block += 1
if block * 50 >= length_of_seqs:
break
handle.write("\n")
class PhylipIterator(AlignmentIterator):
"""Reads a Phylip alignment file returning a MultipleSeqAlignment iterator.
Record identifiers are limited to at most 10 characters.
It only copes with interlaced phylip files! Sequential files won't work
where the sequences are split over multiple lines.
For more information on the file format, please see:
http://evolution.genetics.washington.edu/phylip/doc/sequence.html
http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles
"""
# Default truncation length
id_width = _PHYLIP_ID_WIDTH
_header = None # for caching lines between __next__ calls
def _is_header(self, line):
line = line.strip()
parts = [x for x in line.split() if x]
if len(parts) != 2:
return False # First line should have two integers
try:
number_of_seqs = int(parts[0])
length_of_seqs = int(parts[1])
return True
except ValueError:
return False # First line should have two integers
def _split_id(self, line):
"""Extract the sequence ID from a Phylip line (PRIVATE).
Returning a tuple containing: (sequence_id, sequence_residues)
The first 10 characters in the line are are the sequence id, the
remainder are sequence data.
"""
seq_id = line[: self.id_width].strip()
seq = line[self.id_width :].strip().replace(" ", "")
return seq_id, seq
def __next__(self):
"""Parse the next alignment from the handle."""
handle = self.handle
if self._header is None:
line = handle.readline()
else:
# Header we saved from when we were parsing
# the previous alignment.
line = self._header
self._header = None
if not line:
raise StopIteration
line = line.strip()
parts = [x for x in line.split() if x]
if len(parts) != 2:
raise ValueError("First line should have two integers")
try:
number_of_seqs = int(parts[0])
length_of_seqs = int(parts[1])
except ValueError:
raise ValueError("First line should have two integers") from None
assert self._is_header(line)
if (
self.records_per_alignment is not None
and self.records_per_alignment != number_of_seqs
):
raise ValueError(
"Found %i records in this alignment, told to expect %i"
% (number_of_seqs, self.records_per_alignment)
)
ids = []
seqs = []
# By default, expects STRICT truncation / padding to 10 characters.
# Does not require any whitespace between name and seq.
for i in range(number_of_seqs):
line = handle.readline().rstrip()
sequence_id, s = self._split_id(line)
ids.append(sequence_id)
if "." in s:
raise ValueError(_NO_DOTS)
seqs.append([s])
# Look for further blocks
line = ""
while True:
# Skip any blank lines between blocks...
while "" == line.strip():
line = handle.readline()
if not line:
break # end of file
if not line:
break # end of file
if self._is_header(line):
# Looks like the start of a concatenated alignment
self._header = line
break
# print("New block...")
for i in range(number_of_seqs):
s = line.strip().replace(" ", "")
if "." in s:
raise ValueError(_NO_DOTS)
seqs[i].append(s)
line = handle.readline()
if (not line) and i + 1 < number_of_seqs:
raise ValueError("End of file mid-block")
if not line:
break # end of file
records = (
SeqRecord(Seq("".join(s)), id=i, name=i, description=i)
for (i, s) in zip(ids, seqs)
)
return MultipleSeqAlignment(records)
# Relaxed Phylip
class RelaxedPhylipWriter(PhylipWriter):
"""Relaxed Phylip format writer."""
def write_alignment(self, alignment):
"""Write a relaxed phylip alignment."""
# Check inputs
for name in (s.id.strip() for s in alignment):
if any(c in name for c in string.whitespace):
raise ValueError(f"Whitespace not allowed in identifier: {name}")
# Calculate a truncation length - maximum length of sequence ID plus a
# single character for padding
# If no sequences, set id_width to 1. super(...) call will raise a
# ValueError
if len(alignment) == 0:
id_width = 1
else:
id_width = max(len(s.id.strip()) for s in alignment) + 1
super().write_alignment(alignment, id_width)
class RelaxedPhylipIterator(PhylipIterator):
"""Relaxed Phylip format Iterator."""
def _split_id(self, line):
"""Extract the sequence ID from a Phylip line (PRIVATE).
Returns a tuple containing: (sequence_id, sequence_residues)
For relaxed format split at the first whitespace character.
"""
seq_id, sequence = line.split(None, 1)
sequence = sequence.strip().replace(" ", "")
return seq_id, sequence
class SequentialPhylipWriter(SequentialAlignmentWriter):
"""Sequential Phylip format Writer."""
def write_alignment(self, alignment, id_width=_PHYLIP_ID_WIDTH):
"""Write a Phylip alignment to the handle."""
handle = self.handle
if len(alignment) == 0:
raise ValueError("Must have at least one sequence")
length_of_seqs = alignment.get_alignment_length()
for record in alignment:
if length_of_seqs != len(record.seq):
raise ValueError("Sequences must all be the same length")
if length_of_seqs <= 0:
raise ValueError("Non-empty sequences are required")
# Check for repeated identifiers...
# Apply this test *after* cleaning the identifiers
names = []
for record in alignment:
# Either remove the banned characters, or map them to something
# else like an underscore "_" or pipe "|" character...
name = sanitize_name(record.id, id_width)
if name in names:
raise ValueError(
"Repeated name %r (originally %r), possibly due to truncation"
% (name, record.id)
)
names.append(name)
# From experimentation, the use of tabs is not understood by the
# EMBOSS suite. The nature of the expected white space is not
# defined in the PHYLIP documentation, simply "These are in free
# format, separated by blanks". We'll use spaces to keep EMBOSS
# happy.
handle.write(" %i %s\n" % (len(alignment), length_of_seqs))
for name, record in zip(names, alignment):
sequence = str(record.seq)
if "." in sequence:
raise ValueError(_NO_DOTS)
handle.write(name[:id_width].ljust(id_width))
# Write the entire sequence to one line (see sequential format
# notes in the SequentialPhylipIterator docstring
handle.write(sequence)
handle.write("\n")
class SequentialPhylipIterator(PhylipIterator):
"""Sequential Phylip format Iterator.
The sequential format carries the same restrictions as the normal
interleaved one, with the difference being that the sequences are listed
sequentially, each sequence written in its entirety before the start of
the next. According to the PHYLIP documentation for input file
formatting, newlines and spaces may optionally be entered at any point
in the sequences.
"""
_header = None # for caching lines between __next__ calls
def __next__(self):
"""Parse the next alignment from the handle."""
handle = self.handle
if self._header is None:
line = handle.readline()
else:
# Header we saved from when we were parsing
# the previous alignment.
line = self._header
self._header = None
if not line:
raise StopIteration
line = line.strip()
parts = [x for x in line.split() if x]
if len(parts) != 2:
raise ValueError("First line should have two integers")
try:
number_of_seqs = int(parts[0])
length_of_seqs = int(parts[1])
except ValueError:
raise ValueError("First line should have two integers") from None
assert self._is_header(line)
if (
self.records_per_alignment is not None
and self.records_per_alignment != number_of_seqs
):
raise ValueError(
"Found %i records in this alignment, told to expect %i"
% (number_of_seqs, self.records_per_alignment)
)
ids = []
seqs = []
# By default, expects STRICT truncation / padding to 10 characters.
# Does not require any whitespace between name and seq.
for i in range(number_of_seqs):
line = handle.readline().rstrip()
sequence_id, s = self._split_id(line)
ids.append(sequence_id)
while len(s) < length_of_seqs:
# The sequence may be split into multiple lines
line = handle.readline().strip()
if not line:
break
if line == "":
continue
s = "".join([s, line.strip().replace(" ", "")])
if len(s) > length_of_seqs:
raise ValueError(
"Found a record of length %i, "
"should be %i" % (len(s), length_of_seqs)
)
if "." in s:
raise ValueError(_NO_DOTS)
seqs.append(s)
while True:
# Find other alignments in the file
line = handle.readline()
if not line:
break
if self._is_header(line):
self._header = line
break
records = (
SeqRecord(Seq(s), id=i, name=i, description=i) for (i, s) in zip(ids, seqs)
)
return MultipleSeqAlignment(records)
def sanitize_name(name, width=None):
"""Sanitise sequence identifier for output.
Removes the banned characters "[]()" and replaces the characters ":;"
with "|". The name is truncated to "width" characters if specified.
"""
name = name.strip()
for char in "[](),":
name = name.replace(char, "")
for char in ":;":
name = name.replace(char, "|")
if width is not None:
name = name[:width]
return name
|